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Literature summary extracted from

  • Cahova, H.; Panattoni, A.; Kielkowski, P.; Fanfrlik, J.; Hocek, M.
    5-Substituted pyrimidine and 7-substituted 7-deazapurine dNTPs as substrates for DNA polymerases in competitive primer extension in the presence of natural dNTPs (2016), ACS Chem. Biol., 11, 3165-3171 .
    View publication on PubMed

Application

EC Number Application Comment Organism
2.7.7.7 synthesis the very good competition of 7-substituted 7-deazapurine dNTPs, and still reasonably good activity of 5-substituted pyrimidine dNTPs, in the presence of their natural counterparts is very encouraging for further development of methods of polymerase synthesis of modified DNA and for possible in cellulo and even in vivo applications if satisfactory delivery of modified dNTPs will be solved Geobacillus stearothermophilus
2.7.7.7 synthesis the very good competition of 7-substituted 7-deazapurine dNTPs, and still reasonably good activity of 5-substituted pyrimidine dNTPs, in the presence of their natural counterparts is very encouraging for further development of methods of polymerase synthesis of modified DNA and for possible in cellulo and even in vivo applications if satisfactory delivery of modified dNTPs will be solved Thermococcus kodakarensis
2.7.7.7 synthesis the very good competition of 7-substituted 7-deazapurine dNTPs, and still reasonably good activity of 5-substituted pyrimidine dNTPs, in the presence of their natural counterparts is very encouraging for further development of methods of polymerase synthesis of modified DNA and for possible in cellulo and even in vivo applications if satisfactory delivery of modified dNTPs will be solved Pyrococcus woesei
2.7.7.7 synthesis the very good competition of 7-substituted 7-deazapurine dNTPs, and still reasonably good activity of 5-substituted pyrimidine dNTPs, in the presence of their natural counterparts is very encouraging for further development of methods of polymerase synthesis of modified DNA and for possible in cellulo and even in vivo applications if satisfactory delivery of modified dNTPs will be solved Thermococcus litoralis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.7.7.7 0.0032
-
 TTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0041
-
 7-phenyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0053
-
 dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0056
-
 7-phenyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.006
-
 5-phenyl-dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0061
-
 7-methyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0063
-
 5-ethynyl-dUTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0067
-
 dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0073
-
 7-ethynyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0075
-
 7-ethynyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0079
-
 5-phenyl-dUTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0087
-
 dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0095
-
 7-vinyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0109
-
 7-vinyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0111
-
 7-methyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0125
-
 7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0131
-
 5-vinyl-dUTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0141
-
 5-vinyl-dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 0.0151
-
 5-ethynyl-dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn Geobacillus stearothermophilus
-
 diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn Thermococcus kodakarensis
-
 diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn Pyrococcus woesei
-
 diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn Thermococcus litoralis
-
 diphosphate + DNAn+1
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.7.7.7 Geobacillus stearothermophilus
-
-
-
2.7.7.7 Pyrococcus woesei P61876
-
-
2.7.7.7 Thermococcus kodakarensis
-
-
-
2.7.7.7 Thermococcus litoralis P30317
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.7.7 5-ethynyl-dCTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 5-ethynyl-dUTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 5-phenyl-dCTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 5-phenyl-dUTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 5-vinyl-dCTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 5-vinyl-dUTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 7-deaza-dGTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 7-ethynyl-7-deaza-dATP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 7-ethynyl-7-deaza-dGTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 7-methyl-7-deaza-dATP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 7-methyl-7-deaza-dGTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 7-phenyl-7-deaza-dATP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 7-phenyl-7-deaza-dGTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 7-vinyl-7-deaza-dATP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 7-vinyl-7-deaza-dGTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
-
 Thermococcus kodakarensis diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
-
 Pyrococcus woesei diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn
-
 Thermococcus litoralis diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTP's (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts Thermococcus kodakarensis diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts Pyrococcus woesei diphosphate + DNAn+1
-
 ?
2.7.7.7 a 2'-deoxyribonucleoside 5'-triphosphate + DNAn systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts Thermococcus litoralis diphosphate + DNAn+1
-
 ?
2.7.7.7 dATP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 dCTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 dGTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?
2.7.7.7 TTP + DNAn
-
 Geobacillus stearothermophilus diphosphate + DNAn+1
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.7.7.7 KDO XL DNA polymerase
-
 Thermococcus kodakarensis
2.7.7.7 Vent polymerase
-
 Thermococcus litoralis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.7.7.7 4.6
-
 5-ethynyl-dUTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 5.5
-
 7-methyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 6.1
-
 dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 6.3
-
 7-ethynyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 6.6
-
 TTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 7.1
-
 7-vinyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 7.5
-
 5-phenyl-dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 8
-
 dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 9.3
-
 5-phenyl-dUTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 10.4
-
 5-ethynyl-dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 12.1
-
 7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 12.7
-
 7-methyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 13.1
-
 dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 13.5
-
 7-phenyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 13.7
-
 7-phenyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 13.8
-
 7-vinyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 15.4
-
 5-vinyl-dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 17.5
-
 7-ethynyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 17.7
-
 5-vinyl-dUTP pH and temperature not specified in the publication Geobacillus stearothermophilus

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
2.7.7.7 650
-
 7-vinyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 690
-
 5-ethynyl-dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 730
-
 5-ethynyl-dUTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 880
-
 7-ethynyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 900
-
 7-methyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 910
-
 dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 970
-
 7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 990
-
 dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 1100
-
 5-vinyl-dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 1140
-
 7-methyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 1180
-
 5-phenyl-dUTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 1250
-
 5-phenyl-dCTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 1350
-
 5-vinyl-dUTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 1450
-
 7-vinyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 2060
-
 TTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 2330
-
 7-ethynyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 2410
-
 7-phenyl-7-deaza-dATP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 2470
-
 dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus
2.7.7.7 3340
-
 7-phenyl-7-deaza-dGTP pH and temperature not specified in the publication Geobacillus stearothermophilus